Scores of NHS patients were killed during Britain's deadliest outbreak of a hospital superbug, a damning report by the government's health watchdog reveals today.

The Healthcare Commission attributed the deaths of 90 patients at the Maidstone and Tunbridge Wells hospitals in Kent to infection from Clostridium difficile, which causes severe diarrhoea and has taken over from MRSA as the main threat to patients.

Evidence will be referred to Kent police and the Health and Safety Executive (HSE) about how the trust's slack infection controls contributed to the deaths. They will decide whether to bring criminal charges, which could include murder, manslaughter or breaches of health and safety legislation, said Anna Walker, chief executive of the Healthcare Commission.

This week Alistair Darling, the chancellor, stepped up the fight against hospital-acquired infections by providing £140m in the comprehensive spending review to combat C difficile and £130m to screen all patients coming into hospital for MRSA.

But the commission said the evidence from Maidstone and Tunbridge Wells had national ramifications. It said the cases showed the need for changes in clinical priorities and told the NHS to start treating C difficile as a diagnosis in its own right.

The report found 1,100 patients contracted C difficile at the trust's three hospitals between April 2004 and September 2006. A total of 345 mainly older patients with multiple medical problems died.

The commission concluded that 90 patients "definitely or probably" died as a result of infection. Sixty of these deaths occurred during two outbreaks when the trust failed to introduce adequate counter-measures - the most deadly case of superbug infection in NHS history.

Today's 124-page report blamed the trust's board for giving too much attention to balancing the books and meeting government waiting-time targets - and too little to service to patients and infection control. "Patients, including those with C difficile were often moved between several different wards, increasing the risk of spreading infection," it said.

The investigation began after the C difficile outbreaks, when the trust claimed to have corrected its infection control problems. But the inspectors took photographs of contaminated bedpans, overflowing buckets of needles and sharp instruments, and food stored in medical refrigerators .

The commission said the trust failed to protect patients because the board was unaware of the first outbreak and was slow to react to the second. The government produced a hygiene code for all trusts in October, but the Maidstone board did not discuss it until March. Ms Walker said: "What happened to the patients was a tragedy ... Our inspections suggest infection control is not always prominent enough on the radar of some boards."

The trust said Rose Gibb, its chief executive since 2003, stepped down last week "by mutual agreement". Glenn Douglas, her interim replacement, has promised a zero tolerance approach to infection.

Malcolm Stewart, medical director of the trust, apologised for the tragedy, but could not explain why the hygiene code had been left off the board agenda for five months. He said rates of C difficile in the trust were lower than the NHS average last year.

Peter Carter, general secretary of the Royal College of Nursing, said: "We can only hope that patient care will never be compromised in this way again."

Andrew Lansley, the Conservative health spokesman, said he was shocked by the report and blamed "centrally imposed waiting list targets" for diverting resources away from the protection of patients.